INSTALLATION AND IMPLEMENTATION OF CR-I-TASSER SUITE
   (Copyright 2017 by Zhang Lab, University of Michigan, All rights reserved)
                    (Version 1.0, 2021/01/01)


1. What is CR-I-TASSER Suite?
   
   The CR-I-TASSER Suite is a composite package of programs for protein
   structure prediction guided by cryo-EM density map. 

2. How to run CR-I-TASSER?
   
   a) Main script for running CR-I-TASSER is $pkgdir/I-TASSERmod/runI-TASSER.pl. 
      Run it directly without arguments will output the help information.

   b) Prepare a fasta file with name "seq.fasta" and a density map file in your datadir.

   c) The following arguments must be set (mandatory arguments). One example is: 

      "$pkgdir/I-TASSERmod/runI-TASSER.pl -libdir /home/yourname/ITLIB -seqname example -mapname yourmap.map -datadir /home/yourname/CR-I-TASSER-1.0/example

      -libdir  means the path of the template libraries
      -seqname means the unique name of the computation for your query sequence
      -mapname means the name of input density map (e.g. inputmap.map)
      -datadir means the directory which contains your sequence (seq.fasta) and density map

   d) Other arguments are optional whose default values have been set.
      Arguments such as -python2, -python3 should be defined.
      More details could be found in MANUAL.txt

3. Where are the final predicted results?
   The final results are placed in the same path of your datadir as datadir/model*.pdb. You could
   also check the estimated TM-scores of predicted structures in datadir/etmscore.dat, in which each
   line corresponds to each predicted model.

4. How to install the CR-I-TASSER Suite?

   a) download the CR-I-TASSER Suite 'CR-I-TASSER-1.0.tar.bz2' from
      http://zhanglab.dcmb.med.umich.edu/CR-I-TASSER/download
      and unpack 'CR-I-TASSER-1.0.tar.bz2 by
      > tar -xvf CR-I-TASSER-1.0.tar.bz2
      The root path of this package is called $pkgdir, e.g. 
      /home/yourname/CR-I-TASSER-1.0. You should have all the programs under this 
      directory. You can install the package at any location on your computer.
   
   b) Download CR-I-TASSER library files from
      https://zhanglab.dcmb.med.umich.edu/CR-I-TASSER/download 
      A script 'download_lib.pl' is provided in the package for automated
      library download and update of the libraries.
      We recommend putting the library files under the path /home/yourname/ITLIB.

   c) Third-party software installation:

      While the majority of programs in the package 'CR-I-TASSER-1.0.tar.bz2' are
      developed in the Zhang Lab herein the permission of use is released,
      there are some programs and databases (including blast, nr, GOparser,
      uniclust30,uniref90 and metaclust) which were developed by third-party groups. 
      A default version of blast and nr are included in the package. It is user's obligation to obtain
      license permission from the developers for all the third-party software 
      before using them. In addition, your system needs to have Java, python2, 
      python3 (which supports pytorch >1.1.0) installed.

      More details could be found in MANUAL.txt

5 System requirement:

   a) x86_64 machine, Linux kernel OS, Free disk space of more than 60G.
   b) Perl and java interpreters should be installed. GO:Parser should be installed 
      if you want to predict GO terms
   c) Basic compress and decompress package should be installed to support: 
      tar and bunzip2.
   d) If you are using computer clusters, job management software PBS server should 
      support 'qsub' and 'qstat'. If using other job management software, such as 
      SGE and Slurm, some changes should be made following the instructions at:
      http://zhanglab.dcmb.med.umich.edu/bbs/?q=node/3561

6. Bug report:

   Please report and post bugs and suggestions at CR-I-TASSER message board: 
   http://zhanglab.dcmb.med.umich.edu/forum